This invention relates to scanning a surface and more particularly to such a system which can achieve constant scan length per data sample.
Scanning imaging systems form a map of some characteristic of a surface of interest by exposing the surface to light and measuring a response from the surface. A focused beam of light is moved in a deliberate and repeatable pattern with respect to the surface. The response is generally time-correlated to the position of the scanning beam in order to form a final map of the property with respect to a location on the surface. In most situations, it is important to be able to infer the position of the surface represented by each pixel and to be able to guarantee that the pixel spacing is uniform within some tolerance dictated by the size of the features being scanned.
Relative motion between the light beam and the surface can be achieved by maintaining the surface stationary and moving the beam or, alternatively, keeping the beam stationary while moving the surface. A high performance (high numerical aperture) optical system of reasonable cost, often has a scanner in which a surface moves while the illuminating beam stays in a constant position relative to the beam optics. Such an arrangement results in the desirable property of high numerical aperture. Alternatively, the surface may remain fixed with the light beam being moved. The components that position the surface relative to the beam generally exhibit some systematic position errors that are a function of position or time. These errors degrade the quality of the final map of the desired property with respect to a location on the surface.
The present invention has particular application to gene chips which contain arrays of short DNA chains in an array of sequences bound to a substrate (usually glass). The chip is indexed so that the particular DNA sequence bound in any area is known. A region having a homogeneous composition is referred to as a “feature.” The DNA chips can be incubated with a solution containing RNA or DNA bound to a fluorescent tag, allowing the binding of RNA to individual features. Such systems can be used for the determination of both genotype and gene expression levels.
If fluorescence is observed in a particular region, binding has occurred and a DNA sequence is identified by consulting the index of DNA positions on the chip. The present invention is particularly useful in this context. As will be discussed below, the present invention sets forth a methodology for measuring and compensating position errors which may be a function of position or time to an arbitrary level of linearity.